Background: The Integrated Infectious Disease Capacity-Building Evaluation (IDCAP) was designed to test the effects of two interventions, Integrated Management of Infectious Disease (IMID) training and on-site support (OSS), on clinical practice of mid-level practitioners. This article reports the effects of these interventions on clinical practice in management of common childhood illnesses. Methods: Two trainees from each of 36 health facilities participated in the IMID training. IMID was a three-week core course, two one-week boost courses, and distance learning over nine months. Eighteen of the 36 health facilities were then randomly assigned to arm A, and participated in OSS, while the other 18 health facilities assigned to arm B did not. Clinical faculty assessed trainee practice on clinical practice of six sets of tasks: patient history, physical examination, laboratory tests, diagnosis, treatment, and patient/caregiver education. The effects of IMID were measured by the post/pre adjusted relative risk (aRR) of appropriate practice in arm B. The incremental effects of OSS were measured by the adjusted ratio of relative risks (aRRR) in arm A compared to arm B. All hypotheses were tested at a 5 % level of significance. Results: Patient samples were comparable across arms at baseline and endline. The majority of children were aged under five years; 84 % at baseline and 97 % at endline. The effects of IMID on patient history (aRR = 1.12; 95 % CI = 1.04-1.21) and physical examination (aRR = 1.40; 95 % CI = 1.16-1.68) tasks were statistically significant. OSS was associated with incremental improvement in patient history (aRRR = 1.18; 95 % CI = 1.06-1.31), and physical examination (aRRR = 1.27; 95 % CI = 1.02-1.59) tasks. Improvements in laboratory testing, diagnosis, treatment, and patient/caregiver education were not statistically significant. Conclusion: IMID training was associated with improved patient history taking and physical examination, and OSS further improved these clinical practices. On-site training and continuous quality improvement activities support transfer of learning to practice among mid-level practitioners.